Selective resonant reconfiguration of chemical structures

ABSTRACT

Chemical compositions may be selectively or preferentially excited by the application of scores comprising a series of energy inputs, thereby changing them from a first geometric configuration to a second geometric configuration (e.g., a first to a second stereoisomer).

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is related to and claims the benefit of theearliest available effective filing date(s) from the following listedapplication(s) (the “Related Applications”) (e.g., claims earliestavailable priority dates for other than provisional patent applicationsor claims benefits under 35 USC §119(e) for provisional patentapplications, for any and all parent, grandparent, great-grandparent,etc. applications of the Related Application(s)).

RELATED APPLICATIONS

For purposes of the USPTO extra-statutory requirements, the presentapplication constitutes a continuation-in-part of U.S. patentapplication Ser. No. 11/186,633, entitled SELECTIVE RESONANCE OFCHEMICAL STRUCTURES, naming Muriel Y. Ishikawa, Edward K. Y. Jung,Nathan P. Myhrvold, and Lowell L. Wood, Jr. as inventors, filed Jul. 21,2005, now U.S. Pat. No. 7,979,213, which is currently co-pending, or isan application of which a currently co-pending application is entitledto the benefit of the filing date.

For purposes of the USPTO extra-statutory requirements, the presentapplication constitutes a continuation-in-part of U.S. patentapplication Ser. No. 11/441,786, entitled SELECTIVE RESONANCE OF BODILYAGENTS, naming Muriel Y. Ishikawa, Edward K. Y. Jung, Eric C. Leuthardt,Nathan P. Myhrvold, and Lowell L. Wood, Jr. as inventors, filed May 26,2006, now U.S. Pat. No. 8,195,403, which is currently co-pending, or isan application of which a currently co-pending application is entitledto the benefit of the filing date.

The United States Patent Office (USPTO) has published a notice to theeffect that the USPTO's computer programs require that patent applicantsreference both a serial number and indicate whether an application is acontinuation or continuation-in-part. Stephen G. Kunin, Benefit ofPrior-Filed Application, USPTO Official Gazette Mar. 18, 2003. Thepresent applicant entity has provided above a specific reference to theapplication(s) from which priority is being claimed as recited bystatute. Applicant entity understands that the statute is unambiguous inits specific reference language and does not require either a serialnumber or any characterization, such as “continuation” or“continuation-in-part,” for claiming priority to U.S. patentapplications. Notwithstanding the foregoing, applicant entityunderstands that the USPTO's computer programs have certain data entryrequirements, and hence applicant entity is designating the presentapplication as a continuation-in-part of its parent applications as setforth above, but expressly points out that such designations are not tobe construed in any way as any type of commentary and/or admission as towhether or not the present application contains any new matter inaddition to the matter of its parent application(s).

All subject matter of the Related Applications and of any and allparent, grandparent, great-grandparent, etc. applications of the RelatedApplications is incorporated herein by reference to the extent suchsubject matter is not inconsistent herewith.

SUMMARY

In one aspect, a method for applying energy to a selected group ofproximate atoms within a medium includes selecting a score specifying aseries of differing energy inputs, and applying the series of differingenergy inputs to the medium. The differing energy inputs of thespecified series are selected to resonate respective resonant structuresof a plurality of resonant structures among the group of proximateatoms. At least a subset of the group of proximate atoms changes from afirst geometric configuration to a second geometric configuration inresponse to the applied series of differing energy inputs. The firstgeometric configuration and the second geometric configuration may bestereoisomers. The score may be selected so that the applied series ofdiffering energy inputs has a physical effect. In one approach, thephysical effect may be selected from the group consisting oftransferring substantially more energy to at least a portion of thegroup of proximate atoms than to atoms in the medium that are not partof the group of proximate atoms, breaking a predetermined bond betweentwo members of the group of proximate atoms, and changing a kineticparameter of a reaction involving a member of the group of proximateatoms. Transfer of energy to the medium may be predominantly throughresonant excitation of the plurality of resonant structures. Theplurality of resonant structures may be resonated simultaneously,sequentially, or in a temporally overlapping fashion. The series ofdiffering energy inputs may be applied simultaneously, sequentially, orin a temporally overlapping fashion. The group of proximate atoms mayform at least a portion of a molecule, such as a biomolecule (e.g., aprotein, a nucleotide, or a therapeutic agent such as a plateletactivity modulator), a crystal, and/or a complex of molecules. The groupof proximate atoms may be positioned so that no two members areseparated by a distance of more than 300 Å. In some applications, allmembers of the group of proximate atoms may be connected directly orindirectly by bonds between the atoms (e.g., covalent, ionic, metallic,van der Waals, hydrogen, couloumbic, and/or magnetic attractions). Thescore may comprise at least 4, at least 10, at least 16, or at least 36energy inputs. The plurality of resonant structures may comprise alongitudinal vibrational mode of a bond, a bending mode of two bonds toa member of the group of proximate atoms, and/or a squashing mode of aplurality of bonds between the members of the group of proximate atoms.The score may specify application of an electromagnetic beam, anotherform of electromagnetic energy or another form of energy as an energyinput. For illustrative purposes, the embodiments described herein willrefer to the energy input as a beam or electromagnetic beam, althoughsuch other forms of energy input may be used as appropriate. Theelectromagnetic beam may have at least one characteristic selected fromthe group consisting of a selected set of frequencies (e.g., amonochromatic set, a set comprising a plurality of local maxima, and/orat least two frequencies having differing amplitudes), a selected set ofmodulation frequencies (e.g., at least two frequencies having differingamplitudes), a selected set of phases, a selected set of amplitudes, aselected temporal profile (e.g., a selected beam duration, and/or aselected change in frequency, modulation frequency, phase, amplitude,polarization, and/or direction during a given time interval), a selectedset of polarizations, and/or a selected direction. The electromagneticbeam may be coherent, incoherent, polarized, amplitude modulated, and/orfrequency modulated. It may be an infrared beam. The electromagneticbeam may be scanned. At least one of the energy inputs may comprise aplurality of electromagnetic beams, and the plurality of electromagneticbeams may intersect at a target location. The plurality ofelectromagnetic beams may differ in frequency, modulation frequency,phase, amplitude, temporal profile, polarization, and/or orientation.The method may further include applying a field to the medium that actsto preferentially orient at least a portion of the group of proximateatoms, such as an electric field, a magnetic field, a mechanical stress,a mechanical strain, a lowered or elevated temperature, a lowered orelevated pressure, a phase change, an adsorbing surface, a catalyst,and/or an energy input. The plurality of resonant structures may be inan arrangement having two end resonant structures and a center resonantstructure, where the plurality of resonant structures are resonated in asequence beginning from the two end resonant structures and progressingtowards the center resonant structure (e.g., a temporally overlappingsequence), in which case the group of proximate atoms may undergo aphysical effect upon resonance of the center structure and/or break apredetermined bond between two members of the group of proximate atoms.

In another aspect, a method of exciting a composition including aplurality of resonant structures, each having a resonant frequency,comprises selecting a set of excitation energies and applying the set ofexcitation energies to the composition. Each of the excitation energieshas a frequency matching the resonant frequency of at least one of theresonant structures of the plurality. The set of excitation energies,applied together, causes the composition to change from a firststereoisomer to a second stereoisomer, while any one of the excitationenergies, applied alone, would not cause the change from the firststereoisomer to the second stereoisomer. The frequency may be amodulation frequency. The excitation energies may be appliedsimultaneously, sequentially, or in a temporally overlapping fashion.The composition may be a biomolecule (e.g., a protein, a nucleotide, ora therapeutic agent such as a platelet activity modulator), a crystal,and/or a complex of molecules. The set of excitation energies mayinclude at least 4, at least 10, or at least 36 excitation energies. Theplurality of resonant structures may include a longitudinal vibrationalmode of a bond, a bending mode of two bonds to an atom, and/or asquashing mode of a plurality of bonds. The excitation energies may beelectromagnetic beams, which may have at least at least onecharacteristic selected from the group consisting of a selected set offrequencies (e.g., a monochromatic set, a set comprising a plurality oflocal maxima, a Gaussian set, and/or at least two frequencies havingdiffering amplitudes), a selected set of modulation frequencies (e.g.,at least two frequencies having differing amplitudes), a selected set ofphases, a selected set of amplitudes, a selected temporal profile (e.g.,a selected beam duration, and/or a selected change in frequency,modulation frequency, phase, amplitude, polarization, and/or directionduring a given time interval), a selected set of polarizations, and/or aselected direction. At least one of the electromagnetic beams may becoherent, incoherent, polarized, amplitude modulated, and/or frequencymodulated. It may be an infrared beam. At least one of theelectromagnetic beams may be scanned. At least two of theelectromagnetic beams may differ in frequency, phase, amplitude,temporal profile, polarization, and/or orientation, and/or may intersectat a target location. The method may further include applying a field tothe composition that acts to preferentially orient at least one resonantstructure, such as an electric field, a magnetic field, a mechanicalstress, a mechanical strain, a lowered or elevated temperature, alowered or elevated pressure, a phase change. The plurality of resonantstructures may be in an arrangement having two end resonant structuresand a center resonant structure, where the set of excitation energies isapplied in a sequence beginning from the excitation energies havingfrequencies matching the two end resonant structures and progressingtowards the excitation energy having the frequency matching the centerresonant structure.

In still another aspect, an instrument for exciting chemicalcompositions may include an interpreter, and an energy input component(e.g., a laser). The interpreter converts a score comprising a pluralityof energy input descriptors into control instructions for the energyinput component, which directs energy input into a medium in accordancewith the generated control instructions. The score is selected tospecify inputs that induce a group of proximate atoms to shift from afirst geometric configuration to a second geometric configuration. Eachenergy descriptor may include a description of frequency, modulationfrequency, phase, amplitude, temporal profile, polarization, direction,and/or coherence. The energy input component may include a beam controlelement (e.g., a reflector, a polarizer, an optical fiber, and/or alens) that directs or modifies the beam. The instrument may also includea score location component that selects a score to be converted by theinterpreter. The score location component may select the score from alibrary of scores, each score of the library being associated with oneor more compositions for which the inputs specified by the score inducesa conformational change. The library may be remote from the energy inputcomponent. The interpreter may include a controller that receives thescore from a source. The instrument may also include a monitor incommunication with the controller, and the controller may adjust thescore converted by the interpreter in response to an observation by themonitor. The instrument may also include an input component that allowsa user to specify a score to be converted by the interpreter, and/or aninput component that allows a user to specify a composition or structureand a lookup component that determines a score that describes a set ofenergy inputs expected to induce a conformational change in thespecified composition or structure, and passes the determined score tothe interpreter for conversion. The lookup component may access alibrary of scores associated with composition(s), which may be remotefrom the energy input component. The lookup component may present thescore to the user for approval (e.g., visually or audibly) beforepassing it to the interpreter. Audible presentation may include mappingenergy input frequencies to audible frequencies for playback to theuser.

The foregoing summary is illustrative only and is not intended to be inany way limiting. In addition to the illustrative aspects, embodiments,and features described above, further aspects, embodiments, and featureswill become apparent by reference to the drawings and the followingdetailed description.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A, 1B, and 1C illustrate longitudinal, bending, and squashingmodes, respectively, of resonant structures.

FIG. 2 is a schematic representation of a four-note score.

FIG. 3 illustrates how a frequency of one resonant structure may shiftas another resonant structure is excited.

FIG. 4 is a schematic representation of the response of a molecule to aseries of energy inputs.

FIG. 5 illustrates diagrammatically excitation to breakage of a bond ina linear molecule.

FIG. 6 illustrates diagrammatically the application of multipleintersecting energy inputs to a target voxel.

FIG. 7 is a schematic showing the application of an electric field toalign resonant structures in a medium.

FIG. 8 is a schematic representation of an energy application method.

FIG. 9 is a schematic representation of a device for applying energyaccording to a score.

FIG. 10 is a schematic representation of a device with optionalmonitoring and feedback control for score application.

FIG. 11 is a schematic representation of an apparatus for generatingscore.

FIG. 12 illustrates a system for introducing a chemical agent into amedium.

FIG. 13 is a schematic representation of a library of excitation energyspecifications.

FIG. 14 is the chemical structure of several antiplatelet agents.

DETAILED DESCRIPTION

In the following detailed description, reference is made to theaccompanying drawings, which form a part hereof. In the drawings,similar symbols typically identify similar components, unless contextdictates otherwise. The illustrative embodiments described in thedetailed description, drawings, and claims are not meant to be limiting.Other embodiments may be utilized, and other changes may be made,without departing from the spirit or scope of the subject matterpresented here.

The term “biomolecule,” as used herein, includes without limitationproteins, peptides, amino acids, nucleotides, nucleic acids,carbohydrates, sugars, glycoproteins, lipids, viruses, prions,antibodies, and enzymes, and fragments, derivatives, and modified formsof any of these, and any other naturally-occurring or synthetic moleculeor complex of molecules that has a biological activity or that iseffective in modulating a biological activity.

The term “bond,” as used herein, includes without limitation covalent,ionic, metallic, van der Waals, hydrogen, coulombic, and magneticattractions, as well as any other attractive force between atoms orother particles.

Resonant structures of molecules, crystals, and other compositions haveone or more characteristic resonant frequencies, at which theyrelatively efficiently absorb or otherwise interact with energy appliedat matching frequencies. Spectroscopic techniques exploit thesecharacteristic resonances to extract information about chemicalstructure and properties. For example, covalent bonds typically have acharacteristic frequency of longitudinal vibration which depends insignificant part upon the masses of the atoms forming the bond and thestrength of the bond (e.g., single, double, triple, etc).

FIG. 1A shows a single covalent bond between atoms B and C, which mayvibrate in such a longitudinal mode. Vibration of ionic bonds issimilarly affected by the mass, atomic radius, and charge of the atomsinvolved. Resonant structures may also be formed by groups of bonds,e.g., in bending or squashing modes (shown in FIGS. 1B and 1C,respectively), each with its own characteristic resonant frequency orfrequencies. Crystals may exhibit resonances based on their periodicstructures or other properties. Molecule complexes may have resonancesthat include hydrogen bonds or other attractions between molecules ofthe complex. The characteristic frequencies of any of these structuresmay be shifted by a wide variety of factors, including withoutlimitation the properties of adjacent bonds, the excitation state of themolecule or crystal, the presence of defects in a crystal (e.g., freesurfaces that cause the resonant properties of “quantum dot”crystallites to depend on their size), stresses in the structure,electric or magnetic fields, or other factors that may influence theproperties of the structure. Spectroscopy involves directing energy at atarget, and examining the absorbed, transmitted, reflected, and/oremitted frequency spectrum to characterize the physical properties ofthe target.

Methods are provided herein for directing energy inputs into a target tomanipulate or otherwise interact selectively with its structures. Inparticular, a set of energy inputs analogous to a musical score may beidentified, where different “notes” of the score transfer energy withspatio-temporal selectivity to a target composition, for example byresonating different resonant structures. For scores having a sufficientnumber of notes, high specificity may be obtained, for example whereincompositions having all or most of the corresponding resonant structuresare preferentially excited by “playing the score” to the targetcomposition. Even for “short” scores, energy may be efficientlytransmitted to a target composition that matches most or all of theresonances identified by the score. Notes as used in this descriptionare not limited to representations of frequency. Notes may alsorepresent, without limitation, amplitudes, polarizations, phasecomponents, gradients, or other characteristics of input energies. Whileresonance is an exemplary method of transferring energy that can providespatio-temporal control or other selectivity as discussed below, scoresmay also include energy inputs that transfer energy to molecules in anonresonant fashion. For example one or more optical beams, coherentoptical pulses, or other controllable inputs can transfer energyselectively to particular portions of a molecule and/or at particulartimes.

In one aspect, the scores may be used to characterize or identifycompositions, as an alternative nomenclature to conventional chemicalcomposition and structure notation. Digital or analog processing,visually presenting, or otherwise processing or treating the scores mayindicate or reveal into similarities between compositions that are lessreadily identified using conventional nomenclature.

Scores having desired effects on particular compositions may bedetermined by a variety of methods. One starting point for determining ascore may be to examine a spectrogram of a composition of interest,since the spectrogram reflects certain resonant responses of thecomposition. Alternatively, resonances may be calculated bycomputational methods. Scores may also be determined and/or refined onan empirical basis, using “trial and error” approaches, inferentialapproaches, genetic algorithms, observations of trends or otherempirical approaches. Typically, such approaches would include applyinga candidate score, a portion of a candidate score, or a selected set ofnotes to a composition and observing the corresponding effects, such asenergy absorption, polarization changes, chemical reactions, opticalcharacteristics, vibrations, stresses, changes in electrical or magneticproperties, or other effects. The score, portion of a score, or notesmay be applied at an amplitude level that may differ from the level tobe used in applying the determined score at a later time. For example, asample note may be applied at a significantly higher amplitude as partof the characterization than may be appropriate for later applications.

Scores may have a diverse set of potential effects on variouscompositions. A score may resonate a particular bond in a molecule tobreakage, for example, or it may change a kinetic parameter of anaffected composition or cause local heating in the vicinity of thecomposition. In some embodiments, the scores can act as a form of energycatalyst, preferentially shifting the kinetics of selected chemicalreactions. For example, a score could alter the kinetics of achromatography column, causing a reactant to bind or to unbind inresponse to an applied score. Similarly, a score may alter the migrationrate of composition during an electrophoresis process. In this approach,the score may be used to separate stereoisomers during electrophoresis.

In another example of such a kinetic change, a score may act topreferentially shift a molecule (such as a biomolecule or macromolecule)from one stereoisomer to another. Prokehorenko, et al., “CoherentControl of Retinal Isomerization in Bacteriorhodopsin,” Science313:1257-1261, September 2006, which is incorporated by referenceherein, applies a photoexcitation pulse to preferentially shift theretinal molecule in bacteriorhodopsin from an all-trans to a 13-cisform. By modulating the phases and amplitudes of the spectral componentsof the photoexcitation pulse, the absolute quantity of 13-cis retinalformed on excitation was observed to be enhanced or suppressed by up to20% as compared to a short transform-limited pulse having the sameactinic energy.

Other embodiments include selectively destroying a contaminant or otherunwanted composition, such as removing an undesirable metabolic product(e.g., beta-amyloid plaques in Alzheimer's disease patients, gallstones,or kidney stones), a contaminant (e.g., accumulations of tobacco residuein the lungs), a therapeutic agent not desirable for long-term use(e.g., heparin from the blood of dialysis patients downstream of thedialysis unit), or cell type (e.g., cancerous cells) from living tissue,breaking down pollutants in a smokestack, or selectively destroyingviruses, either in vivo or in vitro. Still other embodiments includeselective repair of biomolecules, e.g., repair of thymine dimers orbreaks in the DNA molecule. Unbound base pairs could be specificallyexcited, or DNA could even be intentionally further damaged in a wayselected to trigger the body's own DNA repair mechanism.

An arrangement of inputs that form a score may be analogized to amusical score to aid in understanding some of the aspects. For example,in one approach a score specifies a set of differing energy inputs thatmay be in sequential, parallel, or other arrangements. These inputs maybe specified in terms of frequency, modulation frequency, phase,amplitude, temporal profile, polarization, direction, and/or coherence.The set of energy inputs may be played in the form of a “melody” (inwhich each energy input ends before or as the next begins), in the formof a “chord” (in which all the energy inputs begin and end together), orin a more complex structure, which may include one or more overlappingenergy inputs. In addition, the specifications for frequency, modulationfrequency, phase, amplitude, polarization, direction, and/or coherencemay change over the duration of an energy input. In some embodiments,the energy inputs are electromagnetic beams, such as infrared, visibleor ultraviolet beams. The electromagnetic beams may be frequency, phase,amplitude, polarization, pulse width, or otherwise modulated. Suchmodulation may be applied to the base frequency of the electromagneticbeam or may be applied to a beam envelope. In another approach that maybe applied independently or in conjunction with the previously describedapproaches, two or more beams may provide more flexibility in supplyingenergy to a selected location, locations, or structures, at frequencies,spatial selectivities, or other parameters, than single sourceapproaches. In one exemplary approach pairs (or larger sets) of inputscan produce beat frequencies, harmonics, interference patterns, or otherconfigurations. In some such configurations and/or combinations, theenergy inputs may have frequencies differing from the resonantfrequencies of the resonant structures, and yet interact appropriatelywith the molecules.

While the previously described approaches have been exemplified in termsof additive combinations of energy inputs, in some embodiments, aportion of the series of energy inputs may interact with structures tonegate, e.g., by damping or cancellation, rather than enhance,vibrations or other interactions with certain resonant structures.Alternatively or in addition, a structure to which it is desired not totransfer energy may be “deactivated” before, or together with, applyingan energy input. For example, the response of the structure may be“deactivated” or otherwise reduced by temporarily bonding it to anotherstructure that changes its resonant frequency or absorbs vibrationalenergy. In other approaches, locally heating the structure, applying amagnetic or electric field, or applying a local or vector stress orpressure, or otherwise interacting with the structure can change itsresonance, or otherwise reduce its response.

When an application of a score involves affecting compositions in amedium (such as but not limited to living tissue), the score may includeelectromagnetic energy inputs in frequency ranges that penetrate themedium. For example, where a material is contained within a container,the frequencies may be selected to correspond to ranges or singlefrequencies where the container is transmissive, yet, the material isresponsive. If desired, suitable modulation or beat frequencies may thenbe used to resonate the resonant structures of the composition.

A schematic of a four-note score illustrating induced changes is shownin FIG. 2. Energy inputs I₁ and I₂ overlap in time, with input I₁beginning before input I₂ begins and ending before input I₂ ends. InputI₁ has a decreasing amplitude with time, while the amplitude of I₂ issubstantially constant. Inputs I₃ and I₄ begin at substantially the sametime, but input I₃ terminates before input I₄. The amplitude of input I₃increases with time while maintaining a constant frequency, while theamplitude of input I₄ stays constant with time while the frequencydecreases. Phase, polarization, direction, and coherence are notspecified in FIG. 2, but each of these properties may similarly changewith time within a single energy input, or differ from one energy inputto another. In particular, phase control between multiple beams mayprovide spatial, temporal, or other specificity that can provideselectivity in resonating only certain structures within a molecule orin targeting molecules having a certain orientation or position.Moreover, polarization of the energy inputs may be useful indistinguishing molecules on the basis of chirality, for example toexcite only molecules having a desired chirality. One skilled in the artwill recognize that other combinations, including a larger number ofenergy inputs or more complex energy inputs may be implemented. Forexample, frequency and amplitude of an energy input may both be varied.As another example, the frequency and/or amplitude of an energy inputmay be increased during one time interval and decreased during another.As still another example, an energy input may be “chopped” to provide asequence of energy input components, which may be periodic or aperiodic.Several other approaches to varying amplitude, frequency, duration orother characteristics of the energy inputs may also be implementedaccording to design and response characteristics of a given application.

In the specific exemplary case where the score is targeted to a specificmolecule (such as a biomolecule or macromolecule) or a set of molecules,the energy inputs of the score will generally correspond to enoughresonant structures in the target molecule to distinguish the targetmolecule from other molecules in its environment (as discussed above,the energy inputs may, but need not, have the same frequencies as theresonant structures to which they correspond). Since most or all of theenergy inputs will resonate the target molecule, while only a subset ofthe energy inputs will resonate other molecules sharing some but not allof the resonant structures of the target, the target will absorb enoughenergy from the score to distinguish it. This effect may cause, forexample, local heating in the area of the target molecule, breaking oneor more bonds in or to the target molecule, or changing a kineticparameter of a reaction involving the molecule.

In many cases, characteristics of systems including one or more atomsand corresponding bonds may be considered independently. In otherapplications, it may be appropriate to analyze, compensate for, adjustfor, or otherwise consider shifts or changes in characteristics of afirst system including one or more atoms responsive to interaction witha second system having one or more atoms or of energy input to the firstsystem of one or more atoms.

For example, one can identify shifts in the resonant longitudinalvibrational frequency of one or more atomic bonds as a result of opticalpower input, as described in for example, in Andrews and Crisp,“Laser-Induced Vibrational Frequency Shift,” bearing a date of 25 Feb.2005, which is incorporated by reference herein and is appended hereto.This effect may be used to tailor the transfer of energy to a molecule,by adjusting the excitation frequency to match the shift as thevibration increases.

FIG. 3 illustrates how the frequency of one resonant structure may shiftas a nearby resonant structure is excited. When inputs R₁ and R₂ areseparately applied (solid lines), they resonate structures atfrequencies f₁ and f₂. However, when the structures are coupled in aparticular composition, the application of input R₁ may shift theresonant frequency f₂ to f₂′. Thus, that particular composition may bemore efficiently excited by resonating with input R₁ and an input R₂′that is frequency shifted relative to input R₂. In a similar approach,the resonant frequency of one resonant structure may shift as theresonant structure is subjected to other influences, such as temperaturechanges or electric or magnetic fields. The energy inputs may be variedto accommodate such variations in a similar fashion.

FIG. 4 illustrates schematically how a score may be used to selectivelyexcite a particular molecule sufficiently to break a bond, which candestroy the molecule. As shown, energy inputs I₁, I₂, I₃, and I₄ areapplied to the composition in a sequence which may include temporaloverlap. Input I₁ excites a first resonant structure, adding energy tothe molecule. As each additional input excites its own respectiveresonant structure in the molecule, the energy added increases as shown,until input I₄ drives the vibration past the breaking strength for abond (shown schematically as dashed line 10). Each of the individualinputs I₁, I₂, I₃, I₄ may be insufficient alone to destroy the molecule,but acting in concert, they do. Where the energy to break the bond ishigher than that which would be provided by a combination of less thanall four inputs (assuming no increase in the amplitudes of theindividual inputs), only molecules having the four resonant structuresin sufficient proximity will experience the breaking of the bond (itwill of course be understood that this technique is not limited toscores specifying exactly four inputs, but that it may be applied withas few as two inputs or as many as appropriate to achieve the finaleffect).

This selectivity can be further enhanced by exploiting frequency shiftsas discussed above, to more selectively interact with molecules whoseresonant structures are responsive to the shifted frequencies. Note thatthe effect of combining respective inputs to provide cumulative energyinput is not limited to breaking bonds as presented in this illustrativeembodiment. For example, the approaches described herein may also beused to alter kinetic parameters, to change a molecule from onestereoisomer to another, or to achieve any other appropriate chemical,physical or other effect.

FIG. 5 illustrates another scenario in which a bond in a molecule havinga substantially linear portion can be excited to breakage. As shown, themolecule includes a chain of atoms A, B, C, D, E, and F. Initially,respective inputs excite the bonds linking atoms A-B and E-F (indicatedwith heavy lines in the uppermost portion of FIG. 5), causing secondaryexcitation and/or frequency shifting of adjacent bonds linking atoms B-Cand D-E. Subsequent inputs excite the adjacent bonds B-C and D-E(indicated with heavy lines in the second tier of FIG. 5).

The excitations of the bonds linking atoms B-C and D-E causes a furtherexcitation and/or frequency shift of center bond linking atoms C-D. Thecumulative effect of the inputs to bonds linking atoms A-B, B-C, D-E,E-F excites the bond linking atoms C-D. In some applications, thecumulative excitation of the bond linking atoms C-D from the adjacentbonds is sufficient to break the bond linking atoms C-D. In some cases,additional excitation directed at the bond linking atoms C-D is combinedwith the cumulative excitation of the bond linking atoms C-D from theadjacent bond to produce the intended result, such as severing the bondlinking atoms C-D. Of course, the technique is not limited to moleculeshaving the simple linear structure shown in FIG. 5, but can be appliedto any composition in which two sequences of resonant structures can beidentified that lead to a common center.

In addition, it may not be necessary to actively excite all of the bondsor other structures along the path to the common center. For example,the excitation of the A-B and E-F bonds shown in FIG. 5 may besufficient to cause secondary excitation of the B-C and/or D-E bondswithout additional energy inputs. In this way, energy inputs targeted toremote structures A-B and E-F may propagate along the molecule, meetingto cause a desired effect at targeted center structure C-D. In suchembodiments, the targeted bond need not be exactly at the midpointbetween the remote structures as shown in FIG. 5; the timing of theexcitation of the remote structures may be adjusted to determine adesired “meeting point” for the propagated excitations.

Moreover, depending upon the amount of energy and the particularcharacteristics of the bonds and atoms, the inputs to excite the variousbonds may be applied substantially simultaneously, may be applied attimes that only overlap partially, or that are non-overlapping. Further,certain resonant structures may be “rung up” and “rung down” in amulti-step process by applying excitation and anti-excitation (e.g.,damping or canceling) energy inputs as discussed above. Controlling therelative timing, intensities, orientations, or other characteristics ofthe plurality of energy inputs according to the ring up response, orother transient response characteristics of the resonant structures canincrease the selectivity, efficiency, or other parameters of energytransfers to or from the resonant structures. Such techniques may alsobe useful to create intermediate structures or effects, analogous to thecreation of intermediate structures in a multi-step chemical synthesisor reaction.

For certain compositions, transfer of energy to the resonant structureswill be a function of the orientation of the resonant structure relativeto the direction of the energy input. FIGS. 6 and 7 illustrate twoembodiments that allow this relative orientation effect to be exploited.

In FIG. 6, three energy inputs I₁, I₂, and I₃ that may be beams ofoptical or non-optical energy from different directions converge at atarget location (voxel) within a medium containing direction-dependentresonant structures. Since the energy inputs arrive from differentdirections, each affects resonant structures in a different orientation.By selecting an appropriate number of energy inputs in differentdirections, an arbitrarily high percentage of the target resonantstructures can be affected by the beams. These energy inputs need not besimultaneously applied from separate sources, as shown in FIG. 6; theymay also be applied by a single source, where either the source or thetarget material is rotated in order to change the effective direction ofthe energy input, or where the single source is redirected by means ofreflectors, beam splitters, optical fibers, applied fields, or otherknown energy directing elements. In addition, the energy input(s) may bescanned relative to the material to affect a plurality of voxels withinthe material. Further, multiple energy inputs need not always intersectas shown in FIG. 6, but may be independently directed according to theneeds of a particular application. The plurality of energy inputs shownmay have either the same or differing frequency, phase, amplitude,temporal profile, polarization, and/or coherence, depending on the needsof the particular application. Multiple energy inputs may also be usedeven with non-direction-dependent structures, for example in order toovercome scattering within the medium. Where a plurality of inputsexcite a given voxel, from differing locations or orientations, theexcitation in the voxel may exceed that of locations outside of thevoxel, thereby allowing selective excitation of the voxel at a selectedlevel.

In another aspect, shown in FIG. 7, an additional influence canactivate, orient, or otherwise influence resonant structures 20 tointeract appropriately with resonant inputs. In the exemplary approachof FIG. 7, an electric field applied to the target material alignsresonant structures 20 prior to application of an energy input. Whilethe exemplary embodiment employs an electric field to influence theresonant structures, any applied field that tends to affect theinteraction of the resonant structures with the energy input may beapplied, including without limitation a magnetic field, an appliedmechanical stress, a lowered or elevated temperature or pressure, aphase change, introduction of an adsorbing surface or catalyst, or theapplication of another energy input. Rotating a number of resonantstructures into a known orientation may allow more efficient excitation,a simpler configuration, or a reduced number of energy inputs (e.g.,only input I₁ as shown in FIG. 7) to resonate the resonant structuresappropriately. As previously described in reference to FIG. 6, theapplied energy input(s) may be scanned, rotated, or otherwise adjustedrelative to the material. In addition, the applied field itself may bescanned, rotated, or otherwise adjusted relative to the target, forexample by movement or rotation of the field or by movement or rotationof the target. In addition to rotating entire molecules or otherresonant structures, portions of molecules may be rotated, for exampleto change configuration from one stereoisomer to another.

FIG. 8 shows schematically a method of applying energy. A suitable scoreis selected by any of a variety of methods, some of which are detailedherein, and then energy is applied to a target in conformance with thescore. For example, in some embodiments, selecting the score may includeone or more of the following steps: identify a selected structure,identify operational and/or functional parameters of the selectedstructure, correlate the selected structure to a stored data set, andretrieve data corresponding to the selected structure. The scorespecifies a plurality of energy inputs that are applied. The energy may,for example, be applied in the form of one or more electromagneticbeam(s), in which case the score may specify frequency, modulationfrequency, phase, amplitude, temporal profile, polarization, and/orcoherence for the beam(s). In some embodiments, applying energy mayinclude one or more of the following steps: producing signalscorresponding to retrieved data, and directing the produced signalstowards a selected structure.

FIG. 9 shows schematically a device for applying energy in accordancewith a score. Interpreter 30 accepts a score which specifies a pluralityof energy inputs. The interpreter may include an electronic controller31 that can receive the score from a source 33, such as a database orlibrary (e.g., the library described below with reference to FIG. 13), afeedback system (e.g., the feedback system described below withreference to FIG. 10), a score generator (e.g., the modeling tooldescribed below with reference to FIG. 11) or other source of a score.The source 33 may be within or integral to the interpreter 30, orexternal to or remote from the interpreter 30.

Additionally, the source 33 may be located proximate to the interpreter,may be separate from the interpreter, or may be distributed. In oneexample, the source may be implemented logic or circuitry that alsoincludes logic or circuitry that forms a part of the interpreter. In oneexample of a distributed source, a remotely located component, such as acentral database, provides information relative to the score that isconverted by a local component, such as a computer, to data appropriatefor use by the interpreter 30. Alternatively, the information relativeto the score may be converted by the electronic controller 31 within theinterpreter, or may be provided to the interpreter in a format notrequiring conversion.

An energy application device may also include a score location component(not shown), which may select a score for conversion by the interpreter,for example from a library of scores, or a score input component (notshown) that accepts a score from a user. In other embodiments, an inputcomponent may accept an input composition or structure (e.g., from auser), and return a score that has an effect on the accepted compositionor structure or on a portion of the accepted composition or structure,to the interpreter. In some embodiments, the input component may thenpresent the returned score to the user for approval before passing it tothe interpreter.

The presented returned score may be represented to the user visually ina variety of manners. For example, the score may be presentedgraphically as a spectrographic representation, a dynamic model, aspreadsheet, or other user perceivable representation. Therepresentation may also include additional information, such as a visualrepresentation of a different score. Such presentation may provide avisually perceivable contrast to the user, for example by highlightingenergy inputs that are added, subtracted, or modified in one scorerelative to another.

In another approach, audio corresponding to the score may be presentedaudibly to the user. In such a case, each note of the score may beconverted to a corresponding audible note that the user can detect. Insome cases, it may be appropriate for the correspondence between thenotes of the score and the presented audible notes to be establishedaccording to a standardized protocol. This can aid a user in detectingpatterns and deviations from such patterns by identifying “off-key”audible notes. In one such protocol, a range of frequencies of the inputenergies can map to a range of audible frequencies, in a linear,logarithmic, or other mapping, such that increases in the input energyfrequency can be represented as increases in the audible frequency.Moreover, intensities or amplitudes may also be mapped to provideaudible indications of the amplitudes of the notes in the score. Oneskilled in the art will recognize that other types of mapping orcorrelations may also be applied. For example, the frequency mapping maybe inverted, the various input frequencies may be mapped into subsets offrequencies (e.g., ranges of input frequencies mapped to selectedoctaves of the audible frequencies), or other types of audiblepresentations may be developed. Further, in addition to, or in lieu of,a signal audible to a user, the score may be mapped to an acousticsignal detectible by an acoustic receiver that can act as a monitor ofthe score components.

In another aspect, the information representing the score may becompressed or encrypted according to known techniques. The interpretermay accept an authorization (e.g., a decryption key or authorizationcode) or may decompress the information to produce a more completerepresentation of the score before continuing the process, as describedbelow.

The interpreter converts the score into appropriate control instructionsfor an energy input device 32 (e.g., one or more lasers, which may bewavelength tunable). The energy input device applies the energy inputs34 to a target 36. The energy input device may apply energy using eithera single or a plurality of beams (e.g., an array of lasers). The energyinput device may further comprise optional elements 38 that directand/or modify the beam (e.g., reflectors, polarizers, optical fibers,lenses, and/or other optical coupling elements).

FIG. 10 shows schematically a device with optional monitoring andfeedback control for score application. A score generator 40 (which mayinclude, for example and without limitation, a database of scores, amolecular modeling device that determines resonant frequencies, adatabase of spectrographs, or another source of scores as describedherein) provides a score to an energy input component 42. The energyinput component applies energy inputs to a target 44 as specified by thescore. In addition, a monitor 46 may observe the effect on the target ofthe applied energy inputs. In embodiments in which a monitor is present,it may optionally provide feedback to the score generator, which maythen provide a new or adjusted score to the energy input component inresponse to the observations of the monitor. The monitor may be of atype that identifies energy levels, kinetic effects, structuralvariations, chemical variations or any other appropriate variation inthe target 44. For example, thermal imaging can provide an indication ofthermal buildup in the target. In another example, an optical beam maypass through or be reflected from the target. As is known, in somematerials, the optical transmission or reflection properties (e.g.,index or refraction, diffraction phenomena, or absorption) can be afunction of stresses, thermal effects, or other effects that may beinduced by the input component 42; the monitor uses the optical beam todetect these changed properties, revealing the effects induced by theinput component.

In biological applications, scores may be used for diagnostic and/ortherapeutic purposes. For example, in embodiments involving thetreatment of blood, a monitoring device may be placed over a bloodvessel (e.g., in the wrist or on the earlobe), continually monitoringand/or altering blood chemistry as blood flows close to the skin.Alternatively, a fiber optic cable or other physical device for energytransmission may deliver energy impulses deeper into the body. In eithercase, a substantial portion, or even all, of the entire volume of bloodof a patient can be treated in a relatively short amount of time as theblood circulates through a targeted vessel. The monitoring device may,for example, observe and/or chemically modify proteins in the blood. Inanother embodiment, the monitoring device may continuously monitor bloodcomponents such as sugars, triglycerides, or cholesterol, and optionallymoderate their levels if they pass a threshold.

FIG. 11 shows schematically an apparatus for generating scores based oncomputational modeling of resonant structures. A modeling tool 50generates a model of a structure (e.g., a molecular model of a chemicalcomposition, or a quantum mechanical model of the energy levels of aquantum dot) in order to determine its predicted resonances. A scoregenerator 52 then incorporates the predicted resonances into a score.The generated score may be passed to an energy input instrument, such asenergy input device 32 described with reference to FIG. 9.

FIG. 12 shows schematically a system for introducing a chemical agentinto a medium, which may in some embodiments be used for therapeuticpurposes. As shown, the chemical agent comprises a composition 60 boundto an optional carrier 62, which is located within a medium 64. Energyinput device 66 applies energy inputs corresponding to a score to themedium. In some embodiments, this score is selected to sever the bondbetween the composition and the carrier, thereby releasing thecomposition into the medium. In other embodiments, the applied scoreactivates the composition directly, for example by breaking one or morebonds of the composition, ablating material surrounding the composition,heating material surrounding the composition, or reacting with materialsurrounding the composition. In some embodiments, these techniques maybe used to deliver a catalyst or other chemical agent todifficult-to-reach areas. For example, a cleaning or recharging agentcould be dispersed throughout a water treatment system in an inert form,and then rendered active by application of a score to the whole system.Such an embodiment may in some cases allow more uniform application ofthe cleaning or recharging agent, particularly in high-surface-areasystems where a reactive agent may be difficult to disperse throughoutthe system.

For use in vivo, the optional carrier or the composition may have anaffinity to a selected substance or tissue, which forms the medium ofFIG. 12. The optional carrier or the composition may be placed directlyin a particular tissue (e.g., by injection into the tissue), or may beintroduced into the body and allowed to accumulate at the selectedtissue. For example, an iodine-containing composition may be introducedinto the body orally or by injection into the bloodstream, and allowedto accumulate in the thyroid gland. A score comprising infrared energyinputs (to which the body is substantially transparent) may then be usedto heat the iodine-containing composition, thereby ablating a tumorand/or a portion of the thyroid gland itself. Other compositions orcarriers may similarly be chosen to accumulate in other tissues (e.g.,calcium in the bones or teeth or organic compounds in the liver), andthen activated by application of a score (e.g., to release a stimulantto cell division and/or growth). Inhaled compositions, optionally boundto fine carriers, may be distributed to the alveoli for treatment of thelungs.

FIG. 13 shows schematically a library of excitation energyspecifications, comprising a structured data repository 70 comprising aplurality of score records. Each score record includes descriptors for aplurality of energy inputs, a descriptor for associated composition(s)affected by the plurality of energy inputs, and optionally a descriptordescribing the effect of the plurality of energy inputs on thecomposition. The energy input descriptors describe at least one offrequency, modulation frequency, phase, amplitude, temporal profile,polarization and direction for each energy input. The library may alsoinclude additional features such as a search engine 72, an inputcomponent 74, and/or an output component 76. If provided, the outputcomponent may provide a user with a score record for download, forexample so that it may be used to direct an energy input device to playthe score in order to affect the associated composition. The library maybe used to screen for a composition, by accessing the library to locatea score record for the composition, applying the energy inputs describedby the energy input descriptors of the score record to a medium, andobserving the medium for reaction of the composition to the appliedinputs. The library may also be used to excite the composition, byaccessing the library to locate a score record for the composition andapplying the energy inputs described by the score record to thecomposition (e.g., to destroy the composition). Alternatively, theselected score record may comprise a descriptor of a composition sharinga functional group with the composition to be excited.

In some embodiments, the compositions to be excited may be agents thathave been or will be administered in vivo, such as but not limited totherapeutic agents (e.g., analgesics, antacids, antianxiety drugs,antiarrhythmics, anticoagulants, anticonvulsants, antidepressants,antidiarrheals, antiemetics, antifungals, antihistamines,antihypertensives, anti-inflammatories, antiplatelet drugs,antipsychotics, antipyretics, antivirals, barbiturates, beta-blockers,bronchodilators, chemotherapy drugs, corticosteroids, coughsuppressants, cytotoxics, decongestants, diuretics, expectorants,hormones, hypoglycemics, immunosuppressives, laxatives, musclerelaxants, sedatives, sex hormones, sleeping drugs, tranquilizers, andvitamins). In many cases, these agents have a well-defined chemicalstructure including functional groups whose resonances can be accuratelymeasured and/or computationally modeled. The selective resonance ofthese agents may serve to catalyze, release, activate, inactivate, ordestroy the agent, depending on the agent and the score applied.Dual-function agents are also envisioned, in which an agent has onetherapeutic effect before application of the score, and is switched toanother therapeutic effect after application of the score.

Certain therapeutic agents may have undesirable side effects, maytrigger allergic reactions, or may have positive effects in some areasof the body and negative effects in others. In some situations, thenegative effects cannot be accurately predicted prior to administrationof the agent. In these cases, the application of a score thatinactivates or destroys the agent may mitigate these negative effects.For example, if a patient experiences an allergic action to anantibiotic, it may be possible to destroy it throughout the patient'ssystem by application of an appropriate score to the body. Inparticular, tetracycline and fluoroquinolone class antibiotics (e.g.,ciprofloxacin and levofloxacin) have specific absorption spectra notcharacteristic of naturally occurring biomolecules, and thus should besusceptible to selective excitation without substantial damage tosurrounding tissue (see, e.g., Lacher, et al., “The Infrared AbsorptionSpectra of Some Antibiotics in Antimony Trichloride Solution,” J. Phys.Chem. 59:610, July 1955, and Albini, et al., “Photophysics andphotochemistry of fluoroquinolones,” Chem. Soc. Rev., 32:238-250, May2003, both of which are incorporated herein by reference). Allergicreactions to fluoroquinolones are infrequent but range from a skin rashthat may be itchy, red, or swollen to life-threatening reactions such assevere difficulty breathing and shock. Allergic reactions totetracycline are also uncommon, but may result in various types of skinrash, and rarely, liver disease. This method of destruction has theadvantage of being substantially noninvasive, and of potentially beingable to reach substantially all of the affected tissue. Therapeuticagents may similarly be partially or fully destroyed in the case of anoverdose.

In another example, a patient receiving a stent may routinely beadministered antiplatelet agents (e.g., clopidogrel, sold under thetrademark PLAVIX, ticlopidine, sold under the trademark TICLID,cilostazol, sold under the trademark PLETAL, abciximab, sold under thetrademark REOPRO, eptifibatide, sold under the trademark INTEGRILIN,tirofiban, sold under the trademark AGGRASTAT, dipyridamole, sold underthe trademark PERSANTINE, or aspirin). While these agents are beneficialin preventing blood from clotting at the site of the stent, they becomea liability if it becomes necessary to operate on the patient, sinceclotting at the incision site will be inhibited. Clopidogrel, inparticular, may require waiting times of as long as two weeks beforesurgery may be performed, which may substantially endanger a patient inneed of emergency treatment. Application of the appropriate score to apatient having clopidogrel in his system may destroy the agent and allowsurgery to be performed substantially sooner. FIG. 14 shows the chemicalstructure of several antiplatelet agents. The thiophene ring present inclopidogrel and in ticlopidine, in particular, is not typical ofbiological structures, and should be susceptible to selective excitationwithout substantial damage to surrounding tissue. Thus, clopidogrel andticlopidine may be broken down and removed from the system in order thatnormal clotting function may be rapidly restored. Similarly,platelet-activating factor 1-O-hexadecyl-2-acetyl-3-thiophosphocholine(AGEPsC) has been synthesized in RP and SP isomers, which have beenmeasured to differ significantly in platelet aggregation activity.(Rosario-Jansen et al., Biochemistry, 27(13):4619-24, 1988, which isincorporated by reference herein). Application of energy inputsaccording to a score that induces a conformal change may be used toshift the balance between more-active and less-active forms of thisagent as appropriate, either in vitro or in vivo.

For humoral agents, a score may be applied to blood as it passes througha dialysis unit, or is otherwise removed from and then returned to thebody. Such embodiments may be useful in situations where the known scorefor an agent includes radiation that may be detrimental to livingtissue, or when preferred inputs are at frequencies to which interveningtissue is substantially opaque.

Some agents (for example, those that have similar structure to naturallyoccurring biomolecules) may require relatively long or complex scores toresonate without substantially affecting ordinary tissue in vivo. Forsuch agents, or for other therapeutic agents for which a score is notknown, is not practical to apply, or is otherwise undesirable, it may beappropriate to append a functional group that can be readily resonated.This group may be used to catalyze, release, activate, inactivate, ordestroy the agent as described above.

In some embodiments, inactive forms of anticlotting agents may beintroduced into the body. These agents may then be activated byapplication of an activating score. The activating score may be appliedonly at selected locations of the body (e.g., in the vicinity of astent) as discussed above, allowing normal clotting action elsewhere inthe body.

In other embodiments, the body may be monitored to determine thequantity or activity of an agent, which may be modulated in response tothe monitor. For example, some pharmaceuticals (e.g., certainimmunosuppressants or chemotherapy agents) have noticeably differentactivities in different patients. These agents may be administeredbeginning in very low doses, and gradually titrated up while monitoringblood levels to reach an optimal concentration without risking anoverdose. However, a patient may have inadequate protection during thetitration process. If the pharmaceutical can be destroyed by applicationof a score to the body, the dose may be more rapidly increased, and anydetected superabundance destroyed, allowing more rapid stabilization atthe desired blood level. In other embodiments, monitoring may be used tomodulate application of a score that activates an agent (e.g., lithium,whose therapeutic blood levels are relatively close to its threshold oftoxicity) from a reservoir of an inactive form of the agent placed inthe body. In either type of system, feedback from the monitor may beused either manually or automatically to establish optimal blood levelsfor the agent.

In some embodiments, it may be desirable to catalyze, release, activate,inactivate, or destroy endogenous agents in the blood or in othertissue. These may include, for example, blood clotting factors (e.g.,prekallikrein, high molecular weight kininogen, any of clotting factorsI-XIII, von Willebrand factor, protein C, protein S, thrombomodulin, orantithrombin III), sugars (e.g., glucose, fructose, sucrose, galactose,mannose, glycerol, or glucuronate), lipids and lipoproteins (e.g.,cholesterol, triglicerides, triacylglycerols, chylomicrons, very lowdensity lipoproteins, low density lipoproteins, intermediate densitylipoproteins, or high density lipoproteins), vitamins, minerals,hormones (e.g., adrenalin, adrenocorticotropic hormone, aldosteron,calcitonin, cortisol, insulin, gastrin, glucagon, glucocorticoids,thyroid hormone, gastrin, secretin, cholecystokinin, somatostatin,neuropeptide Y, other hormones of the gut, thyrotropin-releasinghormone, gonadotropin-releasing hormone, growth hormone-releasinghormone, ghrelin, corticotrophin-releasing hormone, somatostatin,dopamine, antidiuretic hormone, oxytocin, other hormones of thehypothalamus, renin, erythropoietin, calcitrol, other hormones of thekidney, insulin-like growth factor-1, angiotensinogen, thrombopoietin,other hormones of the liver, thyroid-stimulating hormone,follicle-stimulating hormone, luteinizing hormone, prolactin, growthhormone, adrenocorticotropic hormone, antidiuretic hormone, otherhormones of the pituitary, estrogen, testosterone, progesterone,anabolic steroids, other reproductive hormones, melanocyte-stimulatinghormone, parathyroid hormone, melatonin, prolactin, or thyroidhormones), enzymes (e.g., creatine kinase, lactate dehydrogenase,troponin, other cardiac enzymes, aspartate transaminase, alanineaminotransferase, alkaline phosphatase, gamma-glutamyltranspeptidase, orother liver enzymes), antibodies (e.g., antibodies to autoimmunedisorders such as acute transverse myelitis, allergic (Henoch-Schönlein)purpura, alopecia areata, aplastic anemia, brachial neuritis, bullouspemphigoid, dermatitis herpetiformis, polymyositis, dermatomyositis,Eaton-Lambert syndrome, eosinophilic fasciitis, Goodpasture's syndrome,Guillain-Barré syndrome, hemolytic anemia, hepatitis, mixed connectivetissue disease, multiple sclerosis, myasthenia gravis, pemphigus,peripheral ulcerative keratitis, polyglandular deficiency syndrome,relapsing polychondritis, rheumatoid arthritis, scleroderma, Sjögren'ssyndrome, or system lupus erythematosus, or normal antibodies totransplanted materials such as organs, stem cells, or device implants),proteins (e.g., albumins, globulins, fibrinogens, or hemoglobins),including modified, functionalized, and/or synthetic forms of any ofthese.

In some embodiments, the techniques described herein may be applied toliving tissue. In other embodiments, it may be desirable to apply energyaccording to a score to nonliving tissue. It has been reported thatirradiation at wavelengths of 1210 nm or 1720 nm preferentially heatedfat below the surface of skin in pig skin-and-fat tissue samples (see“Free-Electron Laser Targets Fat,” Jefferson Lab News, bearing a date ofApr. 10, 2006, which is incorporated herein by reference). Theapplication of a set of differing energy inputs as described herein mayachieve higher specificity for particular compositions within tissue,whether living or nonliving. Such specificity may be used, for example,to catalyze, release, activate, inactivate, or destroy extrinsic agents(e.g., drugs) or endogenous agents (e.g., viruses) from tissue before itis transplanted into a patient.

Those having skill in the art will recognize that the state of the artof circuit design has progressed to the point where there is typicallylittle distinction left between hardware and software implementations ofaspects of systems. The use of hardware or software is generally adesign choice representing tradeoffs between cost, efficiency,flexibility, and other implementation considerations. Those having skillin the art will appreciate that there are various vehicles by whichprocesses, systems and/or other technologies involving the use of logicand/or circuits can be effected (e.g., hardware, software, and/orfirmware), and that the preferred vehicle will vary with the context inwhich the processes, systems and/or other technologies are deployed. Forexample, if an implementer determines that speed is paramount, theimplementer may opt for a mainly hardware and/or firmware vehicle.Alternatively, if flexibility is paramount, the implementer may opt fora mainly software implementation. In these or other situations, theimplementer may also opt for some combination of hardware, software,and/or firmware. Hence, there are several possible vehicles by which theprocesses, devices and/or other technologies involving logic and/orcircuits described herein may be effected, none of which is inherentlysuperior to the other. Those skilled in the art will recognize thatoptical aspects of implementations may require optically-orientedhardware, software, and or firmware.

The foregoing detailed description has set forth various embodiments,some of which incorporate logic and/or circuits, via the use of blockdiagrams, flow diagrams, operation diagrams, flowcharts, illustrations,and/or examples. Insofar as such block diagrams, operation diagrams,flowcharts, illustrations, and/or examples contain one or morefunctions, operations, or data structures to be performed, manipulated,or stored by logic and/or circuits, it will be understood by thosewithin the art that each such logic and/or circuit can be embodied,individually and/or collectively, by a wide range of hardware, software,firmware, or virtually any combination thereof. For example, someembodiments of the subject matter described herein may be implementedvia Application Specific Integrated Circuits (ASICs), Field ProgrammableGate Arrays (FPGAs), digital signal processors (DSPs), or otherintegrated formats. However, those skilled in the art will recognizethat other embodiments disclosed herein can be equivalently implementedin whole or in part in standard integrated circuits, as one or morecomputer programs running on one or more computers (e.g., as one or moreprograms running on one or more computer systems), as one or moreprograms running on one or more processors (e.g., as one or moreprograms running on one or more microprocessors), as firmware, as analogcircuitry, or as virtually any combination thereof, and that designingthe circuitry and/or writing the code for the software and or firmwarewould be well within the skill of one of skill in the art in light ofthis disclosure. In addition, those skilled in the art will appreciatethat the operations, functions, and data (e.g., scores) described hereinare capable of being distributed or stored in a variety of signalbearing media. Examples of a signal bearing media include, but are notlimited to, recordable type media such as floppy disks, hard diskdrives, CD ROMs, digital tape, and computer memory, and transmissiontype media such as digital and analog communication links using TDM orIP based communication links (e.g., packet links). The choice of signalbearing media will generally be a design choice representing tradeoffsbetween cost, efficiency, flexibility, and other implementationconsiderations in a particular context, and none of these signal bearingmedia is inherently superior to the other.

While various aspects and embodiments have been disclosed herein, otheraspects and embodiments will be apparent to those skilled in the art.The various aspects and embodiments disclosed herein are for purposes ofillustration and are not intended to be limiting, with the true scopeand spirit being indicated by the following claims.

1. A method of exciting a composition including a plurality of resonantstructures, each resonant structure having a respective resonantfrequency, the method comprising: selecting a set of excitationenergies, each excitation energy having a respective amplitude and arespective frequency corresponding to the resonant frequency of at leastone of the resonant structures of the plurality; and applying the set ofexcitation energies to the composition, wherein: the set of excitationenergies, applied together, are selected to induce the composition tochange from a first stereoisomer to a second stereoisomer; and any oneof the excitation energies, applied at its respective amplitude in theabsence of the other members of the set, would not induce a substantialchange from the first stereoisomer to the second stereoisomer.
 2. Themethod of claim 1, wherein the frequency is a modulation frequency. 3.The method of claim 1, wherein the excitation energies are appliedsimultaneously.
 4. The method of claim 1, wherein the excitationenergies are applied sequentially.
 5. The method of claim 1, wherein theexcitation energies are applied in a temporally overlapping fashion. 6.The method of claim 1, wherein the composition is a biomolecule.
 7. Themethod of claim 6, wherein the biomolecule is a protein or a nucleotide.8. The method of claim 6, wherein the biomolecule is a therapeuticagent.
 9. The method of claim 1, wherein the plurality of resonantstructures comprises a longitudinal vibrational mode of a bond.
 10. Themethod of claim 1, wherein the plurality of resonant structurescomprises a bending mode of two bonds to an atom.
 11. The method ofclaim 1, wherein the plurality of resonant structures comprises asquashing mode of a plurality of bonds.
 12. The method of claim 1,wherein the excitation energies are electromagnetic beams.
 13. Themethod of claim 12, wherein at least one of the electromagnetic beams isan infrared beam.
 14. The method of claim 12, wherein at least one ofthe electromagnetic beams is amplitude modulated.
 15. The method ofclaim 12, wherein at least one of the electromagnetic beams is frequencymodulated.
 16. The method of claim 12, further comprising scanning atleast one of the electromagnetic beams.
 17. The method of claim 12,wherein at least two of the electromagnetic beams intersect at a targetlocation.
 18. The method of claim 1, further comprising applying a fieldto the composition, wherein the field acts to preferentially orient atleast one resonant structure.
 19. The method of claim 1, wherein: theplurality of resonant structures are in an arrangement having two endresonant structures and a center resonant structure; and the set ofexcitation energies is applied in a sequence beginning from theexcitation energies having frequencies matching the two end resonantstructures and progressing towards the excitation energy having thefrequency matching the center resonant structure.
 20. The method ofclaim 1, wherein the composition is a crystal.
 21. The method of claim1, wherein the composition is a complex of molecules.
 22. The method ofclaim 1, wherein the set of excitation energies comprises at least 4excitation energies.
 23. The method of claim 1, wherein the set ofexcitation energies comprises at least 10 excitation energies.
 24. Themethod of claim 1, wherein the set of excitation energies comprises atleast 36 excitation energies.
 25. The method of claim 8, wherein thetherapeutic agent is selected to modify clotting activity in blood. 26.The method of claim 12, wherein each electromagnetic beam has at leastone characteristic selected from the group consisting of: a selected setof frequencies; a selected set of phases; a selected set of amplitudes;a selected temporal profile; a selected set of polarizations; and aselected direction.
 27. The method of claim 26, wherein the selected setof frequencies is approximately monochromatic.
 28. The method of claim26, wherein the selected set of frequencies comprises a plurality oflocal maxima.
 29. The method of claim 26, wherein the selected set offrequencies is approximately Gaussian.
 30. The method of claim 26,wherein at least one of the electromagnetic beams is coherent.
 31. Themethod of claim 26, wherein at least one of the electromagnetic beams isincoherent.
 32. The method of claim 26, wherein the selected set offrequencies comprises at least two frequencies, and wherein the at leasttwo frequencies have differing amplitudes.
 33. The method of claim 26,wherein the temporal profile is characterized by a selected beamduration.
 34. The method of claim 26, wherein the temporal profile ischaracterized by a selected change in frequency, phase, amplitude,polarization, or direction during a selected time interval.
 35. Themethod of claim 26, wherein at least one of the electromagnetic beams ispolarized.
 36. The method of claim 12, wherein at least two of theelectromagnetic beams differ in frequency, phase, amplitude, temporalprofile, polarization or orientation.
 37. The method of claim 18,wherein the field is selected from the group consisting of an electricfield, a magnetic field, an electromagnetic field, a mechanical stress,a mechanical strain, a lowered or elevated temperature, a lowered orelevated pressure, a phase change, an adsorbing surface, a catalyst, anexcitation energy, and combinations thereof.